Multiple sequence alignment - TraesCS7D01G461200

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7D01G461200 chr7D 100.000 3304 0 0 1 3304 577593817 577597120 0.000000e+00 6102.0
1 TraesCS7D01G461200 chr7D 92.201 795 58 4 2510 3304 264044315 264043525 0.000000e+00 1122.0
2 TraesCS7D01G461200 chr7B 94.122 2518 123 11 1 2496 640913866 640916380 0.000000e+00 3807.0
3 TraesCS7D01G461200 chr7B 91.667 144 7 2 2349 2487 640942839 640942982 9.350000e-46 195.0
4 TraesCS7D01G461200 chr7B 88.679 106 11 1 1835 1939 640942712 640942817 9.620000e-26 128.0
5 TraesCS7D01G461200 chr7A 93.354 1264 53 13 1 1238 669726790 669728048 0.000000e+00 1840.0
6 TraesCS7D01G461200 chr7A 93.646 1086 34 18 1457 2508 669728118 669729202 0.000000e+00 1591.0
7 TraesCS7D01G461200 chr6A 93.601 797 46 4 2510 3304 499284684 499283891 0.000000e+00 1184.0
8 TraesCS7D01G461200 chr3D 92.965 796 54 2 2510 3304 585231952 585231158 0.000000e+00 1158.0
9 TraesCS7D01G461200 chr3D 90.692 795 70 4 2510 3304 114495276 114496066 0.000000e+00 1055.0
10 TraesCS7D01G461200 chr6D 92.434 793 54 4 2510 3300 408908625 408909413 0.000000e+00 1127.0
11 TraesCS7D01G461200 chr5D 92.085 796 58 5 2510 3304 29148141 29147350 0.000000e+00 1116.0
12 TraesCS7D01G461200 chr2A 91.858 786 58 4 2510 3293 677872497 677873278 0.000000e+00 1092.0
13 TraesCS7D01G461200 chr4D 91.250 800 61 6 2510 3304 380533674 380534469 0.000000e+00 1081.0
14 TraesCS7D01G461200 chr4D 76.163 172 30 10 1065 1229 498949213 498949380 2.730000e-11 80.5
15 TraesCS7D01G461200 chr4B 90.829 796 66 7 2510 3304 460747258 460748047 0.000000e+00 1059.0
16 TraesCS7D01G461200 chr1A 85.976 164 21 2 1065 1227 60537387 60537549 1.220000e-39 174.0
17 TraesCS7D01G461200 chr1D 85.366 164 22 2 1065 1227 62564049 62564211 5.670000e-38 169.0
18 TraesCS7D01G461200 chr1D 95.745 47 2 0 1179 1225 62858095 62858141 3.540000e-10 76.8
19 TraesCS7D01G461200 chr1B 84.756 164 23 2 1065 1227 99709863 99710025 2.640000e-36 163.0
20 TraesCS7D01G461200 chr2D 88.136 59 6 1 1166 1223 95516030 95516088 5.920000e-08 69.4
21 TraesCS7D01G461200 chr2B 88.136 59 6 1 1166 1223 146964099 146964157 5.920000e-08 69.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G461200 chr7D 577593817 577597120 3303 False 6102.0 6102 100.000 1 3304 1 chr7D.!!$F1 3303
1 TraesCS7D01G461200 chr7D 264043525 264044315 790 True 1122.0 1122 92.201 2510 3304 1 chr7D.!!$R1 794
2 TraesCS7D01G461200 chr7B 640913866 640916380 2514 False 3807.0 3807 94.122 1 2496 1 chr7B.!!$F1 2495
3 TraesCS7D01G461200 chr7A 669726790 669729202 2412 False 1715.5 1840 93.500 1 2508 2 chr7A.!!$F1 2507
4 TraesCS7D01G461200 chr6A 499283891 499284684 793 True 1184.0 1184 93.601 2510 3304 1 chr6A.!!$R1 794
5 TraesCS7D01G461200 chr3D 585231158 585231952 794 True 1158.0 1158 92.965 2510 3304 1 chr3D.!!$R1 794
6 TraesCS7D01G461200 chr3D 114495276 114496066 790 False 1055.0 1055 90.692 2510 3304 1 chr3D.!!$F1 794
7 TraesCS7D01G461200 chr6D 408908625 408909413 788 False 1127.0 1127 92.434 2510 3300 1 chr6D.!!$F1 790
8 TraesCS7D01G461200 chr5D 29147350 29148141 791 True 1116.0 1116 92.085 2510 3304 1 chr5D.!!$R1 794
9 TraesCS7D01G461200 chr2A 677872497 677873278 781 False 1092.0 1092 91.858 2510 3293 1 chr2A.!!$F1 783
10 TraesCS7D01G461200 chr4D 380533674 380534469 795 False 1081.0 1081 91.250 2510 3304 1 chr4D.!!$F1 794
11 TraesCS7D01G461200 chr4B 460747258 460748047 789 False 1059.0 1059 90.829 2510 3304 1 chr4B.!!$F1 794

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
930 953 0.745486 TTGAGCCCAGCATCACATCG 60.745 55.000 0.0 0.0 0.0 3.84 F
1316 1375 0.030101 TTGCAAGCACGCCAAGTTAC 59.970 50.000 0.0 0.0 0.0 2.50 F
1352 1411 1.582502 GAGACGGATTAGCAACGTTCG 59.417 52.381 0.0 0.0 41.4 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2207 2269 0.254178 TGAGCTTGAGCAGGGATTCC 59.746 55.000 5.70 0.0 45.16 3.01 R
2210 2272 1.224039 GCTGAGCTTGAGCAGGGAT 59.776 57.895 12.56 0.0 45.16 3.85 R
2593 2699 2.548480 GCGAGCTGTAAGACCTTTTTGT 59.452 45.455 0.00 0.0 34.07 2.83 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.183300 GGTAGGTGCGCACGATCA 59.817 61.111 32.35 15.32 0.00 2.92
118 119 4.696402 AGTTGAACGGTGTAAAACAAGTGA 59.304 37.500 0.00 0.00 0.00 3.41
182 183 3.813443 CGGGGATTGTTGATGAGAAGAT 58.187 45.455 0.00 0.00 0.00 2.40
234 246 7.046033 TCTTTGTTAAGAGGATAAACGGGATC 58.954 38.462 0.00 0.00 35.49 3.36
512 524 5.565592 TCATTTCCACATGCATACAGAAC 57.434 39.130 0.00 0.00 0.00 3.01
551 563 2.031120 CACTGGTGTTTGGATGGTTGT 58.969 47.619 0.00 0.00 0.00 3.32
553 565 3.004315 CACTGGTGTTTGGATGGTTGTAC 59.996 47.826 0.00 0.00 0.00 2.90
554 566 3.218453 CTGGTGTTTGGATGGTTGTACA 58.782 45.455 0.00 0.00 0.00 2.90
556 568 2.295070 GGTGTTTGGATGGTTGTACACC 59.705 50.000 0.00 0.00 45.86 4.16
782 801 2.295885 CATTCCTGTTGGGCTCTCATC 58.704 52.381 0.00 0.00 34.39 2.92
834 853 3.372822 GCATATGAACCGTTCCTTCGAAA 59.627 43.478 6.97 0.00 0.00 3.46
923 946 1.377725 CGAACCTTGAGCCCAGCAT 60.378 57.895 0.00 0.00 0.00 3.79
930 953 0.745486 TTGAGCCCAGCATCACATCG 60.745 55.000 0.00 0.00 0.00 3.84
1011 1039 1.448540 AGGAAACATGAGGCTCGCG 60.449 57.895 10.42 0.00 0.00 5.87
1023 1051 2.182030 CTCGCGGTGGTTCTCCTC 59.818 66.667 6.13 0.00 34.23 3.71
1253 1312 1.421410 GCACGGAGCTTATGTGGTCG 61.421 60.000 13.57 0.00 41.15 4.79
1258 1317 2.034179 CGGAGCTTATGTGGTCGACATA 59.966 50.000 18.91 4.56 43.96 2.29
1259 1318 3.643763 GGAGCTTATGTGGTCGACATAG 58.356 50.000 18.91 5.77 46.15 2.23
1280 1339 5.796350 AGGTGTCTATAAAATTGACGTGC 57.204 39.130 0.00 0.00 37.75 5.34
1282 1341 4.493545 GGTGTCTATAAAATTGACGTGCGG 60.494 45.833 0.00 0.00 37.75 5.69
1315 1374 0.741326 TTTGCAAGCACGCCAAGTTA 59.259 45.000 0.00 0.00 0.00 2.24
1316 1375 0.030101 TTGCAAGCACGCCAAGTTAC 59.970 50.000 0.00 0.00 0.00 2.50
1349 1408 3.324170 CGAGACGGATTAGCAACGT 57.676 52.632 0.00 0.00 44.35 3.99
1352 1411 1.582502 GAGACGGATTAGCAACGTTCG 59.417 52.381 0.00 0.00 41.40 3.95
1359 1418 2.151881 TTAGCAACGTTCGCCAACTA 57.848 45.000 15.85 2.54 0.00 2.24
1376 1435 5.475719 CCAACTAAACTTGTCATACTCGGA 58.524 41.667 0.00 0.00 0.00 4.55
1415 1475 5.856156 AGAAATGTTCATTTTGCCATGACA 58.144 33.333 11.30 0.00 32.68 3.58
1436 1496 2.751166 AAGATCTGACGTTCACTGGG 57.249 50.000 0.00 0.00 0.00 4.45
1453 1513 5.601313 TCACTGGGTAGTTAGGTCCATATTC 59.399 44.000 0.00 0.00 34.07 1.75
1502 1564 2.401766 GGGTTGCGATGCCTCTGTG 61.402 63.158 0.00 0.00 0.00 3.66
1568 1630 3.134127 GTGAACATCGGGCTGGCC 61.134 66.667 10.75 10.75 0.00 5.36
1637 1699 4.008933 GGCGTGGTGTCCTGCTCT 62.009 66.667 0.00 0.00 0.00 4.09
1655 1717 3.785486 CTCTGACATCCTCATTTACGCA 58.215 45.455 0.00 0.00 0.00 5.24
2383 2479 1.573829 GCGGTGTGCGGATTTCTTCA 61.574 55.000 0.00 0.00 0.00 3.02
2395 2491 6.318396 TGCGGATTTCTTCAATAATCATGTGA 59.682 34.615 0.00 0.00 33.43 3.58
2471 2572 5.476091 TGGCAACATATATGTATCACGGA 57.524 39.130 18.56 0.00 46.17 4.69
2508 2613 9.619316 CGGTCTTTCAAATGTATTACAAATGAA 57.381 29.630 17.10 17.10 36.00 2.57
2564 2670 3.990318 CATCATGAAGATGCATGCAGT 57.010 42.857 26.69 13.10 46.90 4.40
2703 2812 9.262240 GTAATAAGAAGGATAAGCTCCCTAGAT 57.738 37.037 3.11 0.00 46.27 1.98
2719 2828 6.875469 TCCCTAGATTCCTATCCTATTGTGT 58.125 40.000 0.00 0.00 0.00 3.72
2802 2911 1.068352 ACCAAAGGCTCCCTGGAGTT 61.068 55.000 14.45 0.00 43.70 3.01
2840 2949 0.742505 CCACGTACGGATCCAAGCTA 59.257 55.000 21.06 0.00 0.00 3.32
3033 3147 3.264450 ACTGGAGGACTAATGTTGAAGGG 59.736 47.826 0.00 0.00 0.00 3.95
3068 3182 5.298989 TCTCCAAAGTAACTTGGCAAGTA 57.701 39.130 31.34 17.24 44.79 2.24
3152 3267 4.457466 TCCTACCCATCGCCTTTTAATTC 58.543 43.478 0.00 0.00 0.00 2.17
3154 3269 4.642885 CCTACCCATCGCCTTTTAATTCAA 59.357 41.667 0.00 0.00 0.00 2.69
3250 3365 2.223688 CCAAATGTGCAACGACCTTGAA 60.224 45.455 0.00 0.00 42.39 2.69
3295 3410 7.941795 ATCCGTATAGAAAGATTTTACCGTG 57.058 36.000 0.00 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 0.250234 ATGCGCCGGATATATGTGCT 59.750 50.000 5.05 0.00 36.51 4.40
135 136 1.772063 GCCACACGTTTGTTCTCGCT 61.772 55.000 0.36 0.00 31.66 4.93
234 246 0.242825 TGGTACTTTGACTCGCGAGG 59.757 55.000 36.93 22.27 0.00 4.63
533 545 3.004315 GTGTACAACCATCCAAACACCAG 59.996 47.826 0.00 0.00 32.94 4.00
551 563 4.922471 TCCAATTATCGATCACGGTGTA 57.078 40.909 0.00 0.00 40.21 2.90
553 565 3.679980 GGATCCAATTATCGATCACGGTG 59.320 47.826 6.95 0.56 37.26 4.94
554 566 3.323691 TGGATCCAATTATCGATCACGGT 59.676 43.478 13.46 0.00 37.26 4.83
556 568 5.170748 TGATGGATCCAATTATCGATCACG 58.829 41.667 20.67 0.00 42.56 4.35
557 569 6.019237 CGATGATGGATCCAATTATCGATCAC 60.019 42.308 32.97 18.40 46.86 3.06
559 571 6.276091 TCGATGATGGATCCAATTATCGATC 58.724 40.000 33.91 22.96 39.12 3.69
644 661 2.119801 ATTGCTGATCTGGTCACACC 57.880 50.000 1.46 0.00 39.22 4.16
649 666 1.541233 CGGGGTATTGCTGATCTGGTC 60.541 57.143 1.46 0.00 0.00 4.02
691 710 1.894466 TGAAAATGTGATGCTGTGGGG 59.106 47.619 0.00 0.00 0.00 4.96
834 853 3.025262 TGGTTTTCCGCACCTACTTTTT 58.975 40.909 0.00 0.00 44.36 1.94
923 946 0.678950 TGCTTGGTGAGACGATGTGA 59.321 50.000 0.00 0.00 0.00 3.58
930 953 3.261933 GCTGCTGCTTGGTGAGAC 58.738 61.111 8.53 0.00 36.03 3.36
1011 1039 2.435059 GCGCAGAGGAGAACCACC 60.435 66.667 0.30 0.00 38.94 4.61
1107 1138 3.329889 TTCTCCACGCCCCTGCAT 61.330 61.111 0.00 0.00 37.32 3.96
1258 1317 4.328983 CGCACGTCAATTTTATAGACACCT 59.671 41.667 0.00 0.00 32.68 4.00
1259 1318 4.493545 CCGCACGTCAATTTTATAGACACC 60.494 45.833 0.00 0.00 32.68 4.16
1315 1374 2.293399 GTCTCGGTTCATTTTTGCCAGT 59.707 45.455 0.00 0.00 0.00 4.00
1316 1375 2.665519 CGTCTCGGTTCATTTTTGCCAG 60.666 50.000 0.00 0.00 0.00 4.85
1347 1406 2.285756 TGACAAGTTTAGTTGGCGAACG 59.714 45.455 5.91 0.00 38.41 3.95
1349 1408 5.302360 AGTATGACAAGTTTAGTTGGCGAA 58.698 37.500 2.66 0.00 38.41 4.70
1352 1411 4.092968 CCGAGTATGACAAGTTTAGTTGGC 59.907 45.833 2.66 0.00 35.83 4.52
1389 1449 5.927689 TCATGGCAAAATGAACATTTCTCAC 59.072 36.000 12.20 5.63 39.88 3.51
1393 1453 6.542574 TTGTCATGGCAAAATGAACATTTC 57.457 33.333 11.03 2.76 39.88 2.17
1415 1475 3.181454 ACCCAGTGAACGTCAGATCTTTT 60.181 43.478 0.00 0.00 0.00 2.27
1419 1479 2.492484 ACTACCCAGTGAACGTCAGATC 59.508 50.000 0.00 0.00 32.25 2.75
1422 1482 2.814280 AACTACCCAGTGAACGTCAG 57.186 50.000 0.00 0.00 34.36 3.51
1453 1513 8.776470 TGCATGCATATGATCGTTATATTATGG 58.224 33.333 18.46 0.00 36.36 2.74
1568 1630 3.068691 TCCAGGAGGTCGAAGGCG 61.069 66.667 0.00 0.00 39.35 5.52
1637 1699 2.279741 GCTGCGTAAATGAGGATGTCA 58.720 47.619 0.00 0.00 40.38 3.58
1685 1747 0.948623 CGTCGAAGTGGATGTTGCCA 60.949 55.000 0.00 0.00 35.02 4.92
1808 1870 1.660575 CACGTCGAAGTCCTTGCGT 60.661 57.895 0.00 0.00 0.00 5.24
1940 2002 0.465460 GGTGGCACTTGTGGTTGAGA 60.465 55.000 18.45 0.00 0.00 3.27
2198 2260 1.878522 CAGGGATTCCGCGAAGTCG 60.879 63.158 8.23 0.00 43.27 4.18
2207 2269 0.254178 TGAGCTTGAGCAGGGATTCC 59.746 55.000 5.70 0.00 45.16 3.01
2210 2272 1.224039 GCTGAGCTTGAGCAGGGAT 59.776 57.895 12.56 0.00 45.16 3.85
2395 2491 9.059260 CAAAAGAATGGATTGAACCAGAAAAAT 57.941 29.630 0.00 0.00 43.49 1.82
2406 2503 7.332557 CAATGGGAATCAAAAGAATGGATTGA 58.667 34.615 0.00 0.00 37.47 2.57
2593 2699 2.548480 GCGAGCTGTAAGACCTTTTTGT 59.452 45.455 0.00 0.00 34.07 2.83
2633 2741 7.870445 TCAGCATGTATTTTCCCTTTTGTTTAC 59.130 33.333 0.00 0.00 37.40 2.01
2634 2742 7.870445 GTCAGCATGTATTTTCCCTTTTGTTTA 59.130 33.333 0.00 0.00 37.40 2.01
2638 2746 5.782047 TGTCAGCATGTATTTTCCCTTTTG 58.218 37.500 0.00 0.00 37.40 2.44
2649 2758 3.873361 CGGTTGATCTTGTCAGCATGTAT 59.127 43.478 0.00 0.00 39.57 2.29
2703 2812 3.492656 GCGCTCACACAATAGGATAGGAA 60.493 47.826 0.00 0.00 0.00 3.36
2719 2828 4.812476 CGGTTCGGATGGCGCTCA 62.812 66.667 7.64 3.81 0.00 4.26
2802 2911 4.279145 GTGGTCCTTACTCACTCCTATGA 58.721 47.826 0.00 0.00 0.00 2.15
2840 2949 3.048600 TGCAGGTTATCTTCAGGGCTAT 58.951 45.455 0.00 0.00 0.00 2.97
3033 3147 9.530633 AGTTACTTTGGAGAACGATTCATATAC 57.469 33.333 0.00 0.00 0.00 1.47
3068 3182 6.655078 ACAACACTTATTTCTTGATTGCCT 57.345 33.333 0.00 0.00 0.00 4.75
3200 3315 6.440436 TCAAGGTTCCTTTGCGTATTAAAAC 58.560 36.000 0.86 0.00 0.00 2.43
3250 3365 5.129320 GGATTTGATTAATTCTGGCCCACTT 59.871 40.000 0.00 0.00 0.00 3.16


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.